Prevalence of Plasmodium falciparum parasites harbouring chloroquine-resistant but not artemisinin-resistant alleles in Busia County, Western Kenya.

Abstract

Background: The recent emergence of Plasmodium falciparum parasites harbouring kelch 13 mutations associated with artemisinin partial resistance (ART-R) in sub-Saharan Africa is a major concern. Regular molecular epidemiological surveys are recommended to monitor the level of mutant parasites associated with drug resistance.

Objective: To analyse single nucleotide polymorphisms (SNPs) in P. falciparum genes associated with resistance to antimalarial drugs in blood samples collected from malaria patients prior to treatment in Busia County, Western Kenya, using a highly multiplexed deep amplicon sequencing protocol.

Methods: Parasite DNA was extracted from dried blood spots (DBS) collected from patients attending health facilities along the Kenya-Uganda border, in Busia County. A highly multiplexed deep amplicon sequencing protocol was applied to analyze SNPs in genes associated with antimalarial drugs resistance.

Results: Out of 118 analysed samples, Pfkelch13 mutations were identified in 6 (5.1%) samples. All the six samples harboured A578S, one of the most frequently detected Pfkelch13 mutations in Africa, which does not confer ART-R. The data also indicated that 11% (13) of the samples had mutant Pfcrt alleles, with 62% harbouring the triple mutant haplotype, CVIET. In contrast, 98% of the samples had dhfr mutations at positions N51I, C59R, or S108N alleles. All the samples carried mutations in the dhps gene with a high prevalence of the single A437G mutation (84%) and a lower frequency of double or triple mutations. Further analysis revealed absence of deletions in the Pfhrp2, with no mutations at Pfmdr1 codons 86 or 1246, both of which are associated with chloroquine resistance.

Conclusion: These findings show absence of validated Pfkelch13 markers associated with ART-R in Busia County, Western Kenya. Although chloroquine-sensitive (wild-type) parasites are widely circulating, sulfadoxine-pyrimethamine-sensitive parasites remain rare. Continued large scale genomic surveillance studies are essential to detect emerging resistance and guide malaria treatment strategies in the region.